This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We model the fragmentation of a peptide with a probabilistic model trained on high-quality tandem mass spectrometry data and use this model to predict spectra. These predicted spectra have higher similarity to experimentally acquired spectra than those predicted by an in-house implementation of the mobile-proton algorithm. In addition, a search using the spectra predicted by the model has increased sensitivity and specificity compared to a search with the spectra used by SEQUEST.